3I8V

Crystal structure of human PDE4a with 4-(3-butoxy-4-methoxyphenyl)methyl-2-imidazolidone

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	14-20%(w/v) PEG3350, 5-10%(v/v) glycerol, 100mM Tris-HCl, 200mM Magnesium acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.406	α = 90
b = 105.406	β = 90
c = 165.252	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315	double Si 111 crystal monochromator	2009-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.25	45.33	100	0.068	12.8	7.03		44862		2	40

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.33	100		0.326	4.3	7.11	4383

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2QYK	2.25	45.33	42599	2262	99.94	0.18908	0.18732	0.22171	RANDOM	38.352

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.25			-0.25		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.571
r_dihedral_angle_4_deg	20.97
r_dihedral_angle_3_deg	15.237
r_dihedral_angle_1_deg	4.671
r_scangle_it	3.298
r_scbond_it	2.028
r_angle_refined_deg	1.297
r_mcangle_it	1.197
r_mcbond_it	0.598
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5406
Nucleic Acid Atoms
Solvent Atoms	349
Heterogen Atoms	63

Software

Software
Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling